Salmonid Genome Duplication Drives Specialization and Adaptation

全基因组复制（WGD）很可能在进化创新中发挥更重要的作用。 在植物、动物、基底脊椎动物（约5亿年）、鱼类（约3亿年）和最近的祖先鲑科动物（约9亿年）中发现了这种广泛的复制。 这些主要的基因组扩增使遗传原材料加倍，这些原材料与对各种环境的全新适应有关，并可能在新物种和谱系的进化中发挥关键作用。 WGD和重大进化事件之间的联系似乎与进化史上的开创性转变有关。 我们在未来五年的具体目标是：1）建立在我们最近开发的高质量大西洋鲑鱼基因组参考序列的基础上，以探索北极红点鲑、银鲑和奇努克鲑鱼的功能性染色体结构和基因变化，并进一步注释大西洋鲑鱼内的重复基因，2）对鲑科鱼类外群北方派克鱼基因组进行功能注释，并对其染色体结构和一个新的性别决定系统进行表征。 待研究的染色体结构特征包括DNA甲基化、组蛋白修饰和DNA开放性，我们将比较这些潜在的表观遗传特征与基因表达模式。 表观遗传学的主题是有争议的，并继续发展。 染色质结构和DNA甲基化模式可以从一代传递到下一代，环境因素可以改变这些模式。 表观遗传变化可以导致非常快速（和可逆）的表型变化和适应快速变化的环境。 该提案探讨了这一问题，在鲑鱼和梭子鱼，我们试图注释新开发的鲑鱼和梭子鱼基因组，通过映射这些网站，并将它们连接到基因启动子和基因表达模式。 我们还将探索一种最近进化的新的，可能是在北美梭子鱼中发现的环境修饰的性别决定模式。

Whole genome duplications (WGD) very likely play one of the more significant roles in evolutionary innovation. Such expansive duplications are found in plants, animals, in basal vertebrates (~500MYA), fishes (~300MYA), and more recently in ancestral salmonids (~90MYA). These major genome expansions double the genetic raw material that has been associated with radically new adaptations to various environments and likely play a key role in the evolution of novel species and lineages. A connection between WGDs and major evolutionary events appears to be linked to seminal shifts in evolutionary history. Our specific objectives over the next 5 years are to: 1) build on our recent development of a high quality Atlantic salmon genome reference sequence to explore functional chromosomal structural and gene changes in Arctic charr, Coho and Chinook salmon, and further annotate duplicate genes within the Atlantic salmon, and 2) develop functional annotation for the salmonid outgroup Northern Pike genome and characterize its chromosome structure and a novel sex-determining system. Chromosome structural characteristics to be explored include DNA methylation, histone modification, and DNA openness and we will compare these potential epigenetic features with gene expression patterns. The subject of epigenetics is controversial and continues to evolve. Chromatin structure and DNA methylation patterns can be passed from one generation to the next and environmental factors can modify such patterns. Epigenetic changes can cause very rapid (and reversible) phenotypic changes and adaptation to a rapidly changing environment. This proposal explores this subject in salmonids and pike where we seek to annotate newly developed salmonid and pike genomes by mapping these sites and linking them to gene promoter and gene expression patterns. We will also explore a very recently evolved novel and possibly environmentally modified sex-determining pattern found in North American pike.